From my memory - I could be wrong in some parts: I think if you wanted an item with *2* different "recolorable" colors, you had to ensure that for instance the green would only be 8 different shades and the brown would only be 16 different shades.
Then, in the .PAL file, put them at specific places (and of course your graphic would need to consider this updated .PAL file then). This was one of the features of ZT Studio.